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how to specify fixed angle
- gandhiforbes
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7 years 11 months ago #110
by gandhiforbes
Dear Sir,
In my simulation, i am trying to keep the angle 'fixed'.
I am defining in the following way:
angles
C2 N1 C5
Angle 108.25642
Constant fixed
with this, i am getting the following error:
Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
At line 1310 of file participation.f90 (unit = 204, file = ' QY2')
Fortran runtime error: File already opened in another unit
Done...
Traceback (most recent call last):
file '/................................................/library_setup.py", line 561, in <module>
temp_regid.append(nbr_angles = = nbr_angles_fixed)
NameError: name 'nbr_angles' is not defined.
Is my representation correct?
How to solve this error?
Thanks.
Anand.
In my simulation, i am trying to keep the angle 'fixed'.
I am defining in the following way:
angles
C2 N1 C5
Angle 108.25642
Constant fixed
with this, i am getting the following error:
Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
At line 1310 of file participation.f90 (unit = 204, file = ' QY2')
Fortran runtime error: File already opened in another unit
Done...
Traceback (most recent call last):
file '/................................................/library_setup.py", line 561, in <module>
temp_regid.append(nbr_angles = = nbr_angles_fixed)
NameError: name 'nbr_angles' is not defined.
Is my representation correct?
How to solve this error?
Thanks.
Anand.
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- ryangmullen
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7 years 11 months ago #111
by ryangmullen
Dear Anand,
The procedure to create the files required for a Cassandra simulation are as follows:
1) Create an .mcf file. The python script mcfgen.py is provided to help with this step:
a) Run
> python mcfgen.py molecule.pdb --ffTemplate
to generate an intermediate file molecule.ff.
b) Fill out molecule.ff with the parameters found in the literature.
c) Run
> python mcfgen.py molecule.pdb
2) Create an input file using the options specified in the user manual, for example nvt.inp
3) Create a fragment library. The python script library_setup.py is provided to help with this step:
a) Run
> library_setup.py /home/applications/cassandra.exe nvt.inp molecule.pdb
It appears that you are getting the error you report on step 3a. Can you confirm that you have completed steps 1a-c and step 2 before running step 3a? In particular, is the .mcf file you generated in step 1c listed in the input file you created in step 2?
Ryan
The procedure to create the files required for a Cassandra simulation are as follows:
1) Create an .mcf file. The python script mcfgen.py is provided to help with this step:
a) Run
> python mcfgen.py molecule.pdb --ffTemplate
to generate an intermediate file molecule.ff.
b) Fill out molecule.ff with the parameters found in the literature.
c) Run
> python mcfgen.py molecule.pdb
2) Create an input file using the options specified in the user manual, for example nvt.inp
3) Create a fragment library. The python script library_setup.py is provided to help with this step:
a) Run
> library_setup.py /home/applications/cassandra.exe nvt.inp molecule.pdb
It appears that you are getting the error you report on step 3a. Can you confirm that you have completed steps 1a-c and step 2 before running step 3a? In particular, is the .mcf file you generated in step 1c listed in the input file you created in step 2?
Ryan
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- gandhiforbes
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7 years 11 months ago #112
by gandhiforbes
Dear Sir,
I am trying to reproduce the results of the paper: Thermodynamic properties of the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate from Monte Carlo simulations,Green Chemistry, 2002, 4, 112–118.
I have followed the follwing steps:
1) Made two pdb files: bmim.pdb and pf6.pdb (considering United approach).
2) Run the command:
$ python mcfgen.py bmim.pdb --ffTemplate
This created bmim.ff file.
$ python mcfgen.py pf6.pdb --ffTemplate
This created pf6.ff file.
3) force field parameters were taken from literature. kept bond lengths and angle terms constant.
4) Run the command:
$ python mcfgen.py bmim.pdb
This created bmim.mcf file.
$ python mcfgen.py pf6.pdb
This created pf6.mcf file.
5) Created an input file npt.inp
6) Run the command:
$ python library_setup.py /home/anand/Downloads/flareGet/Compressed/Cassandra_V1.1/Src/cassandra_gfortran.exe npt.inp bmim.pdb pf6.pdb
I am getting the following messages:
*********Cassandra setup*********
Cassandra location: /home/anand/Downloads/flareGet/Compressed/Cassandra_V1.1/Src/cassandra_gfortran.exe
Scanning input file...
Number of species found: 2
The MCF file number 1 is: bmim.mcf
The MCF file number 2 is: pf6.mcf
Species 1 has 4 fragments
Species 2 has 1 fragments
Molecules with rings found.
These are:
Species 1 has 1 rings.
Species 2 has 0 rings.
Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
At line 1310 of file participation.f90 (unit = 204, file = ' QY2')
Fortran runtime error: File already opened in another unit
MCF generation file not created for species 1.
Fragment configuration will be taken from PDB file.
Done...
Traceback (most recent call last):
File "library_setup.py", line 561, in <module>
temp_rigid.append(nbr_angles == nbr_angles_fixed)
NameError: name 'nbr_angles' is not defined
I am attaching all the files.
I am trying to reproduce the results of the paper: Thermodynamic properties of the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate from Monte Carlo simulations,Green Chemistry, 2002, 4, 112–118.
I have followed the follwing steps:
1) Made two pdb files: bmim.pdb and pf6.pdb (considering United approach).
2) Run the command:
$ python mcfgen.py bmim.pdb --ffTemplate
This created bmim.ff file.
$ python mcfgen.py pf6.pdb --ffTemplate
This created pf6.ff file.
3) force field parameters were taken from literature. kept bond lengths and angle terms constant.
4) Run the command:
$ python mcfgen.py bmim.pdb
This created bmim.mcf file.
$ python mcfgen.py pf6.pdb
This created pf6.mcf file.
5) Created an input file npt.inp
6) Run the command:
$ python library_setup.py /home/anand/Downloads/flareGet/Compressed/Cassandra_V1.1/Src/cassandra_gfortran.exe npt.inp bmim.pdb pf6.pdb
I am getting the following messages:
*********Cassandra setup*********
Cassandra location: /home/anand/Downloads/flareGet/Compressed/Cassandra_V1.1/Src/cassandra_gfortran.exe
Scanning input file...
Number of species found: 2
The MCF file number 1 is: bmim.mcf
The MCF file number 2 is: pf6.mcf
Species 1 has 4 fragments
Species 2 has 1 fragments
Molecules with rings found.
These are:
Species 1 has 1 rings.
Species 2 has 0 rings.
Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
At line 1310 of file participation.f90 (unit = 204, file = ' QY2')
Fortran runtime error: File already opened in another unit
MCF generation file not created for species 1.
Fragment configuration will be taken from PDB file.
Done...
Traceback (most recent call last):
File "library_setup.py", line 561, in <module>
temp_rigid.append(nbr_angles == nbr_angles_fixed)
NameError: name 'nbr_angles' is not defined
I am attaching all the files.
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- ryangmullen
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- gandhiforbes
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